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Table 1 Haplotype calls from 454 (run 1) and cloning/Sanger (CS) sequencing.

From: Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

Method 454 CS 454 CS 454 CS 454 454 454 454 454 CS
Amplicon F2 S1 F5 S2 F5 S2 F4 F6 F7 F8 Total
MSV HCs 1-2 # # 6-8 # # 7-10a* # # 3-5 # 11-15 # 16-18 # 19-24 # HCs #
C0140 GA 1.566 112 TCC 664 136 CCGgGc 1.491 81 TAT 582 CCTCG 867 TCG 888 CTACCG 542   
  GG 583 36     CCGaGc 431 55 CAT 390 CCTAG 816 TTA 288 TCTTTA 195   
  CA 528 30        TAC 382        10.213 450
C0766 GG 1.525 114 TCC 360 140 CCGgGc 1.084 147 TAC 1.679   nd TCG 1.878 CTACCG 876   
  CA 842 41 CCC 195 48 CCGgAc 506 41 CAT 601        9.546 531
C0913 CA 1.869 113 TCC 680 132 CCGgGc 1.221 145 TAC 1.556 CCTCG 1.195 TCG 1.816 CTACCG 2.153   
  GA 1.157 58 CCC 287 54 CCGgAc 617 41 TCC 634 CCTAG 593      13.778 543
NA12760 GA 1.750 92 TCC 795 99 CCGgGc 1.566 104 TAC 2.825 CCTCG 1.669 TTA 2.056 TCTTTA 645   
  GG 386 20 CCC 181 60 CCGgAc 339 55 TAT 981 CTCAC 599 TCG 1.696 CTACCG 605   
  CA 319 19 CTG 184 0 TGGgAc 459 0 TCC 797 CCTAG 499      18.351 449
NA15029 GA 1.530   TCC 767 nd CCGgGc 1.046 nd TCC 1.156 CCTGC 1.785 TTA 1.689 TCTTTA 377   
  GG 805      CCAgGc 431   TAT 882 CTCAT 1.087 TCG 1.115 CTACCG 267   
     CTG 475   TGGgAc 913   TAC 496         
           CAT 420        15.241  
NA15213 GA 1.326   TCC 665 nd CCGgGc 1.338 nd TAC 278 CCTCG 1.178 TCG 1.496 CTACCG 929   
  CA 349   CTG 171   TGGgAc 390   TAT 98 CCTAG 577 TTA 866 TCTTTA 551   
           TCC 87 CTCAT 473      10.772  
NA15385 GA 985   TCC 374 nd CCGgGc 702 nd TAC 1.374 CCTCG 1.003 TCG 938 CTACCG 688   
  GG 592   CCC 169   CCGgAc 239   TAT 673 CCTAG 322 TTA 782 TCTTTA 483   
     CTG 88   TGGgAc 188   TCC 345 CTCAT 280      10.225  
NA18502 GA 812 80 TCC 182 125 CCGgGc 265 139 TAT 1.453 CCTCG 415 TTA 856 TCTTTA 645   
  CA 561 58 CCC 21 15 CCGgGa 56 0    TTCAT 65 TCG 418 CTACCG 267   
     CCG (7) 0 CGGgAc 39 0          5.995 402
NA18552 CA 3.490   TCC 197 nd CCGgGc 273 nd TAT 225 CCTCG 1.653 TCG 1.756 CTACCG 1.525   
     CCC 328   CCGgAc 340   TAC 1.058         
           CAT 503        11.348  
NA18858 GA 677 97 TCC 1.234 188 CCGgGc 623 124 TAT 1.490 CCTCG 1.327 TTA 1.087 TCTTTA 2.404   
  CA 324 45     CCGaGc 218 51 TAC 822    TCG 404 CTACCG 633   
  GG 205 (16)                11.448 505
NA19140 GA 314 57 TCC 706 nd CCGgGc 234 nd   nd CCTCG 504 TTA 281   nd   
  CA 310 73     CCGaGc 42     CTCAT 130 TCG 62     
  GG 105 24                2.688 154
Total   22.910 1.069   8.702 982   15.012 983   21.787   17.037   20.372   13.785 119.605 3.034
  1. #: number of HCs; *: alleles in lower cases refer to the 2 additionally identified MSVs 9a and 10a; (): nominally below 10% threshold; nd: no data.
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